rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
282,DRR179616,DRX170142,DRS185505,DRP007318,PRJDB8340,Gene expression analysis of zebrafish fin melanophores and xanthophores.,DRP007318,Other,Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.,,,Biological replicate 2,Fin xanthophore 03,SAMD00172019,,sample name:Zebrafish pigment cell 06|cell type:Xanthophore|collection date:2015 11 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin,,,,,,,,,Ion Torrent PGM sequencing of SAMD00172019,DRX170142,Zebrafish fin xanthophore 01,1,1,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>232</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP007318,Ion Torrent PGM sequencing of SAMD00172019,,,,376558775.0,1624500.0,DRR179616,0:231.80,A:107837072;C:79508449;G:79372899;T:109840355;N:0,231,,,,107837072,79508449,79372899,109840355,0,DRX170142,DRS185505,DRA008445,"OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University","Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University",1,0.86944,,0.10951,,0.90425,,0.59385,,311,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,other,smarter,bulk,unknown,unknown,,Japan,2021-05-21,Adult,Adult,Fin,Surface Structure
283,DRR179615,DRX170141,DRS185504,DRP007318,PRJDB8340,Gene expression analysis of zebrafish fin melanophores and xanthophores.,DRP007318,Other,Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.,,,Biological replicate 1,Fin xanthophore 02,SAMD00172018,,sample name:Zebrafish pigment cell 05|cell type:Xanthophore|collection date:2015 09 10|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin,,,,,,,,,Ion Torrent PGM sequencing of SAMD00172018,DRX170141,Zebrafish fin xanthophore 01,1,1,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>243</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP007318,Ion Torrent PGM sequencing of SAMD00172018,,,,515115515.0,2124170.0,DRR179615,0:242.50,A:138421982;C:119032803;G:119412227;T:138248503;N:0,242,,,,138421982,119032803,119412227,138248503,0,DRX170141,DRS185504,DRA008445,"OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University","Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University",1,0.88998,,0.05858,,0.88051,,0.50917,,284,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,other,smarter,bulk,unknown,unknown,,Japan,2021-05-21,Adult,Adult,Fin,Surface Structure
284,DRR179614,DRX170140,DRS185503,DRP007318,PRJDB8340,Gene expression analysis of zebrafish fin melanophores and xanthophores.,DRP007318,Other,Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.,,,Biological replicate 1,Fin xanthophore 01,SAMD00172017,,sample name:Zebrafish pigment cell 04|cell type:Xanthophore|collection date:2015 09 10|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin,,,,,,,,,Ion Torrent PGM sequencing of SAMD00172017,DRX170140,Zebrafish fin xanthophore 01,1,1,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>247</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP007318,Ion Torrent PGM sequencing of SAMD00172017,,,,371242152.0,1504407.0,DRR179614,0:246.77,A:99341086;C:86126839;G:86264882;T:99509345;N:0,246,,,,99341086,86126839,86264882,99509345,0,DRX170140,DRS185503,DRA008445,"OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University","Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University",1,0.88672,,0.06422,,0.85679,,0.5066,,56,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,other,smarter,bulk,unknown,unknown,,Japan,2021-05-21,Adult,Adult,Fin,Surface Structure
285,DRR179613,DRX170139,DRS185502,DRP007318,PRJDB8340,Gene expression analysis of zebrafish fin melanophores and xanthophores.,DRP007318,Other,Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.,,,Biological replicate 2,Fin melanophore 03,SAMD00172016,,sample name:Zebrafish pigment cell 03|cell type:Melanophore|collection date:2015 11 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin,,,,,,,,,Ion Torrent PGM sequencing of SAMD00172016,DRX170139,Zebrafish fin melanophore 03,1,1,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>248</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP007318,Ion Torrent PGM sequencing of SAMD00172016,,,,342802993.0,1585538.0,DRR179613,0:216.21,A:90833658;C:80789744;G:80463233;T:90716358;N:0,216,,,,90833658,80789744,80463233,90716358,0,DRX170139,DRS185502,DRA008445,"OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University","Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University",1,0.8312,,0.03528,,0.88605,,0.47299,,285,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,other,smarter,bulk,unknown,unknown,,Japan,2021-05-21,Adult,Adult,Fin,Surface Structure
286,DRR179612,DRX170138,DRS185501,DRP007318,PRJDB8340,Gene expression analysis of zebrafish fin melanophores and xanthophores.,DRP007318,Other,Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.,,,Biological replicate 1,Fin melanophore 02,SAMD00172015,,sample name:Zebrafish pigment cell 02|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin,,,,,,,,,Ion Torrent PGM sequencing of SAMD00172015,DRX170138,Zebrafish fin melanophore 02,1,1,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>216</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP007318,Ion Torrent PGM sequencing of SAMD00172015,,,,538412675.0,2168231.0,DRR179612,0:248.32,A:147128403;C:121854818;G:121564109;T:147865345;N:0,248,,,,147128403,121854818,121564109,147865345,0,DRX170138,DRS185501,DRA008445,"OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University","Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University",1,0.89106,,0.07081,,0.89286,,0.5935,,283,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,other,smarter,bulk,unknown,unknown,,Japan,2021-05-21,Adult,Adult,Fin,Surface Structure
287,DRR179611,DRX170137,DRS185500,DRP007318,PRJDB8340,Gene expression analysis of zebrafish fin melanophores and xanthophores.,DRP007318,Other,Pigment cells  melanophores and xanthophores were collected from zebrafish fin. Total RNAs were extracted from each melanophore and xanthophore  and cDNA libraries were prepared using SMARTer Ultra Low Input RNA Kit for Sequencing v3 and Ion Xpress Plus gDNA Fragment Library Preparation. The libraries were sequenced using the Ion PGM with Ion PGM OT2 400 kit and Ion PGM Sequencing 400 kit.,,,Biological replicate 1,Fin melanophore 01,SAMD00172014,,sample name:Zebrafish pigment cell 01|cell type:Melanophore|collection date:2015 05 12|dev stage:Adult|genotype:Wild type|tissue:Caudal fin and anal fin,,,,,,,,,Ion Torrent PGM sequencing of SAMD00172014,DRX170137,Zebrafish fin melanophore 01,1,1,,RNA-Seq,TRANSCRIPTOMIC,RT-PCR,SINGLE,ION_TORRENT,Ion Torrent PGM,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>215</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,DRP007318,Ion Torrent PGM sequencing of SAMD00172014,,,,282446840.0,1311431.0,DRR179611,0:215.37,A:74927237;C:66575483;G:66161471;T:74782649;N:0,215,,,,74927237,66575483,66161471,74782649,0,DRX170137,DRS185500,DRA008445,"OSAKA_FB|Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University","Laboratory Pattern Formation, Graduate School of Frontier Biosciences, Osaka University",1,0.85938,,0.0335,,0.89248,,0.58813,,274,,B,,usable mapping rate,ion_torrent,ion_torrent,full_length,other,smarter,bulk,unknown,unknown,,Japan,2021-05-21,Adult,Adult,Fin,Surface Structure
15504,ERR757154,ERX701784,ERS659467,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Normalization across length,SAMEA3251321,UNIVERSITY OF AMSTERDAM,ENA first public:2015 02 12|ENA last update:2015 02 12|External Id:SAMEA3251321|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2015 02 12T17:06:49Z|INSDC last update:2015 02 12T09:52:20Z|INSDC status:public|Submitter Id:Female X|common name:zebrafish|dev stage:Adult|sample name:Female X|sex:female,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 2,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2015 02 12|ENA LAST UPDATE:2018 11 16,RID0035_003.fastq.gz,fastq,275591336.0,7611054.0,ena RUN UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 2,0:36.21,A:72212971;C:63331647;G:68054270;T:71992448;N:0,36,,,,72212971,63331647,68054270,71992448,0,ERX701784,ERS659467,ERA410345,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.76262,,0.4273,,0.8101,,0.56676,,8,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2015-02-12,Adult,Adult,Undetermined,Undetermined
15505,ERR757153,ERX701783,ERS659466,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Normalization across length,SAMEA3251320,UNIVERSITY OF AMSTERDAM,ENA first public:2015 02 12|ENA last update:2015 02 12|External Id:SAMEA3251320|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2015 02 12T17:06:49Z|INSDC last update:2015 02 12T09:52:20Z|INSDC status:public|Submitter Id:Female 002|common name:zebrafish|dev stage:Adult|sample name:Female 002|sex:female,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 1,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2015 02 12|ENA LAST UPDATE:2018 11 16,RID0035_006.fastq.gz,fastq,193706106.0,6343893.0,ena RUN UNIVERSITY OF AMSTERDAM 12 02 2015 09:52:08:968 1,0:30.53,A:52756888;C:42895374;G:46979869;T:51073975;N:0,30,,,,52756888,42895374,46979869,51073975,0,ERX701783,ERS659466,ERA410345,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74991,,0.41319,,0.83002,,0.55823,,8,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2015-02-12,Adult,Adult,Undetermined,Undetermined
15506,ERR647638,ERX604074,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 7,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_007.fastq.gz,fastq,181485343.0,7581675.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 7,0:23.94,A:49408107;C:35660562;G:44520624;T:51896050;N:0,23,,,,49408107,35660562,44520624,51896050,0,ERX604074,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75831,,0.16017,,0.90723,,0.48684,,13,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15507,ERR647632,ERX604068,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 1,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_001.fastq.gz,fastq,158714692.0,5407747.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 1,0:29.35,A:42098161;C:32991434;G:38596553;T:45028544;N:0,29,,,,42098161,32991434,38596553,45028544,0,ERX604068,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75901,,0.20293,,0.89505,,0.48215,,24,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15508,ERR647636,ERX604072,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 5,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_005.fastq.gz,fastq,124167412.0,4838491.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 5,0:25.66,A:33439510;C:24728035;G:30897675;T:35102192;N:0,25,,,,33439510,24728035,30897675,35102192,0,ERX604072,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.76027,,0.17783,,0.89692,,0.48421,,30,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15509,ERR647635,ERX604071,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 4,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_004.fastq.gz,fastq,124786630.0,4701452.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 4,0:26.54,A:33803418;C:24800330;G:30482560;T:35700322;N:0,26,,,,33803418,24800330,30482560,35700322,0,ERX604071,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74872,,0.18448,,0.89789,,0.50377,,12,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15510,ERR647634,ERX604070,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 3,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_003.fastq.gz,fastq,110526752.0,4078127.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 3,0:27.10,A:29453167;C:22981184;G:27444083;T:30648318;N:0,27,,,,29453167,22981184,27444083,30648318,0,ERX604070,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73961,,0.1804,,0.89686,,0.50069,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15511,ERR647633,ERX604069,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 2,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_002.fastq.gz,fastq,114721515.0,4468497.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 2,0:25.67,A:31387085;C:22123581;G:28270438;T:32940411;N:0,25,,,,31387085,22123581,28270438,32940411,0,ERX604069,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75767,,0.17199,,0.90118,,0.49949,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15512,ERR647645,ERX604081,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 14,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_014.fastq.gz,fastq,127742942.0,5487454.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 14,0:23.28,A:35700746;C:25577569;G:31187339;T:35277288;N:0,23,,,,35700746,25577569,31187339,35277288,0,ERX604081,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.72451,,0.1507,,0.91078,,0.47283,,30,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15513,ERR647644,ERX604080,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 13,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_013.fastq.gz,fastq,175319872.0,7193103.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 13,0:24.37,A:48008107;C:34657005;G:43047489;T:49607271;N:0,24,,,,48008107,34657005,43047489,49607271,0,ERX604080,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75539,,0.16288,,0.90388,,0.47538,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15514,ERR647643,ERX604079,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 12,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_012.fastq.gz,fastq,177443752.0,7567733.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 12,0:23.45,A:48143286;C:36300870;G:44060167;T:48939429;N:0,23,,,,48143286,36300870,44060167,48939429,0,ERX604079,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74839,,0.15018,,0.90782,,0.49076,,27,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15515,ERR647642,ERX604078,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 11,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_011.fastq.gz,fastq,163389373.0,6320373.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 11,0:25.85,A:44540588;C:32608476;G:40066295;T:46174014;N:0,25,,,,44540588,32608476,40066295,46174014,0,ERX604078,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75948,,0.17375,,0.90252,,0.47536,,33,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15516,ERR647641,ERX604077,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 10,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_010.fastq.gz,fastq,128059692.0,5701206.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 10,0:22.46,A:35418188;C:24802528;G:31593786;T:36245190;N:0,22,,,,35418188,24802528,31593786,36245190,0,ERX604077,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.72586,,0.1331,,0.92514,,0.4216,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15517,ERR647637,ERX604073,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:678 6,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_006.fastq.gz,fastq,165327404.0,6835740.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 6,0:24.19,A:45252916;C:32442683;G:40306020;T:47325785;N:0,24,,,,45252916,32442683,40306020,47325785,0,ERX604073,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74944,,0.16,,0.91068,,0.47704,,21,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15518,ERR647640,ERX604076,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 9,RID0015,Reproducibility,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_009.fastq.gz,fastq,134426587.0,5846482.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 9,0:22.99,A:36803811;C:26283055;G:33442229;T:37897492;N:0,22,,,,36803811,26283055,33442229,37897492,0,ERX604076,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74219,,0.13958,,0.91837,,0.47819,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15519,ERR647639,ERX604075,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 8,RID0015,Fold Change,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0015_008.fastq.gz,fastq,164369360.0,6762174.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:26:05:679 8,0:24.31,A:44826982;C:33030972;G:40615427;T:45895979;N:0,24,,,,44826982,33030972,40615427,45895979,0,ERX604075,ERS557914,ERA363852,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75513,,0.16254,,0.90534,,0.50535,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15520,ERR647623,ERX604059,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 8,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_008.fastq.gz,fastq,198146766.0,7373392.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 8,0:26.87,A:50518864;C:42346985;G:50683068;T:54597849;N:0,26,,,,50518864,42346985,50683068,54597849,0,ERX604059,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73719,,0.16567,,0.89869,,0.49695,,76,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15521,ERR647622,ERX604058,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 7,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_007.fastq.gz,fastq,240260456.0,9194064.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 7,0:26.13,A:62434032;C:50861577;G:60916218;T:66048629;N:0,26,,,,62434032,50861577,60916218,66048629,0,ERX604058,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73042,,0.17017,,0.89509,,0.51784,,44,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15522,ERR647620,ERX604056,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 5,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_005.fastq.gz,fastq,140470735.0,4903805.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 5,0:28.65,A:35312706;C:29191443;G:36788541;T:39178045;N:0,28,,,,35312706,29191443,36788541,39178045,0,ERX604056,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.76081,,0.16609,,0.90216,,0.48155,,72,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15523,ERR647617,ERX604053,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 2,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_002.fastq.gz,fastq,113953599.0,4875815.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 2,0:23.37,A:29576305;C:23096908;G:29656780;T:31623606;N:0,23,,,,29576305,23096908,29656780,31623606,0,ERX604053,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.70891,,0.13528,,0.91208,,0.4622,,24,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15524,ERR647624,ERX604060,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 9,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_009.fastq.gz,fastq,127769435.0,5492615.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 9,0:23.26,A:34397217;C:25332113;G:31991788;T:36048317;N:0,23,,,,34397217,25332113,31991788,36048317,0,ERX604060,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.71147,,0.1472,,0.91015,,0.49014,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15525,ERR647629,ERX604065,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 14,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_014.fastq.gz,fastq,83983757.0,3823842.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 14,0:21.96,A:22501534;C:16455147;G:21619305;T:23407771;N:0,21,,,,22501534,16455147,21619305,23407771,0,ERX604065,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.70211,,0.13351,,0.92038,,0.45898,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15526,ERR647631,ERX604067,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 16,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_016.fastq.gz,fastq,117220472.0,4272650.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 16,0:27.44,A:29509123;C:25768315;G:30220006;T:31723028;N:0,27,,,,29509123,25768315,30220006,31723028,0,ERX604067,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.68585,,0.14679,,0.90778,,0.49492,,20,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15527,ERR647618,ERX604054,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 3,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_003.fastq.gz,fastq,165279016.0,5211580.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 3,0:31.71,A:41451579;C:36699133;G:41477197;T:45651107;N:0,31,,,,41451579,36699133,41477197,45651107,0,ERX604054,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.71827,,0.17456,,0.90554,,0.50274,,18,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15528,ERR647621,ERX604057,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 6,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_006.fastq.gz,fastq,181164500.0,7686285.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 6,0:23.57,A:48622049;C:36019225;G:45318073;T:51205153;N:0,23,,,,48622049,36019225,45318073,51205153,0,ERX604057,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73267,,0.15948,,0.9026,,0.483,,14,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15529,ERR647619,ERX604055,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 4,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_004.fastq.gz,fastq,131702671.0,4688094.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 4,0:28.09,A:32537215;C:28853793;G:34317576;T:35994087;N:0,28,,,,32537215,28853793,34317576,35994087,0,ERX604055,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.68635,,0.14911,,0.90532,,0.50027,,31,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15530,ERR647628,ERX604064,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 13,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_013.fastq.gz,fastq,123881257.0,5143681.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 13,0:24.08,A:32852368;C:25503683;G:31339781;T:34185425;N:0,24,,,,32852368,25503683,31339781,34185425,0,ERX604064,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.72384,,0.15147,,0.90648,,0.46,,24,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15531,ERR647627,ERX604063,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 12,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_012.fastq.gz,fastq,135155439.0,6123293.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 12,0:22.07,A:35870227;C:27070386;G:34401412;T:37813414;N:0,22,,,,35870227,27070386,34401412,37813414,0,ERX604063,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.69126,,0.12647,,0.91695,,0.46572,,25,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15532,ERR647626,ERX604062,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 11,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_011.fastq.gz,fastq,138836612.0,5648801.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 11,0:24.58,A:36426455;C:28359755;G:34985736;T:39064666;N:0,24,,,,36426455,28359755,34985736,39064666,0,ERX604062,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73565,,0.15718,,0.90382,,0.45772,,67,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15533,ERR647625,ERX604061,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 10,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_010.fastq.gz,fastq,182404716.0,6612019.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 10,0:27.59,A:47718609;C:38775928;G:45637186;T:50272993;N:0,27,,,,47718609,38775928,45637186,50272993,0,ERX604061,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75246,,0.19746,,0.88544,,0.48212,,36,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15534,ERR647616,ERX604052,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:086 1,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_001.fastq.gz,fastq,137653436.0,5155975.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 1,0:26.70,A:34561717;C:29961559;G:35320222;T:37809938;N:0,26,,,,34561717,29961559,35320222,37809938,0,ERX604052,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.71887,,0.15223,,0.90824,,0.49462,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15535,ERR647630,ERX604066,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 15,RID0017,EtOH conc. experiment,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0017_015.fastq.gz,fastq,101714594.0,4045987.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 15:08:22:087 15,0:25.14,A:26518632;C:20741074;G:25853629;T:28601259;N:0,25,,,,26518632,20741074,25853629,28601259,0,ERX604066,ERS557914,ERA363851,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74566,,0.16455,,0.89534,,0.48977,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15536,ERR647610,ERX604046,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent PGM sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 1,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent PGM,,ERP007147,Ion Torrent PGM sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0023_009.fastq.gz,fastq,114880508.0,4321457.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 1,0:26.58,A:31499097;C:23030789;G:27803371;T:32547251;N:0,26,,,,31499097,23030789,27803371,32547251,0,ERX604046,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.7932,,0.2086,,0.89045,,0.49364,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15537,ERR647611,ERX604047,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 2,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0023_010.fastq.gz,fastq,124380158.0,4885304.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 2,0:25.46,A:33809369;C:25116497;G:30529372;T:34924920;N:0,25,,,,33809369,25116497,30529372,34924920,0,ERX604047,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78302,,0.1944,,0.89398,,0.50469,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15538,ERR647612,ERX604048,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 3,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0023_011.fastq.gz,fastq,122081664.0,4959591.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 3,0:24.62,A:33452935;C:24151113;G:29942213;T:34535403;N:0,24,,,,33452935,24151113,29942213,34535403,0,ERX604048,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.77425,,0.18982,,0.8911,,0.46046,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15539,ERR647615,ERX604051,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 6,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0023_014.fastq.gz,fastq,120491210.0,4564333.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 6,0:26.40,A:33116448;C:24416657;G:29447901;T:33510204;N:0,26,,,,33116448,24416657,29447901,33510204,0,ERX604051,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.77843,,0.20568,,0.88605,,0.51892,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15540,ERR647614,ERX604050,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 5,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0023_013.fastq.gz,fastq,108193052.0,4221217.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 5,0:25.63,A:29795112;C:21481151;G:26281164;T:30635625;N:0,25,,,,29795112,21481151,26281164,30635625,0,ERX604050,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78861,,0.19966,,0.89207,,0.49332,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15541,ERR647613,ERX604049,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 4,RID0023,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0023_012.fastq.gz,fastq,134807115.0,5232713.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:59:02:785 4,0:25.76,A:37141537;C:27086121;G:32486547;T:38092910;N:0,25,,,,37141537,27086121,32486547,38092910,0,ERX604049,ERS557914,ERA363850,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78328,,0.20061,,0.88903,,0.51655,,32,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15542,ERR647603,ERX604039,ERS557923,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Female 016,SAMEA2796308,UNIVERSITY OF AMSTERDAM,Alias:Female 016|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:25Z|INSDC status:public|SRA accession:ERS557923|Sample Name:ERS557923|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 8,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_010.fastq.gz,fastq,186445198.0,6054478.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 8,0:30.79,A:51431122;C:41043403;G:44213690;T:49756983;N:0,30,,,,51431122,41043403,44213690,49756983,0,ERX604039,ERS557923,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74649,,0.44738,,0.84254,,0.55199,,13,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15543,ERR647602,ERX604038,ERS557922,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Female 014,SAMEA2796307,UNIVERSITY OF AMSTERDAM,Alias:Female 014|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:25Z|INSDC status:public|SRA accession:ERS557922|Sample Name:ERS557922|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 7,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_009.fastq.gz,fastq,199860614.0,6227225.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 7,0:32.09,A:53999848;C:44698032;G:48251471;T:52911263;N:0,32,,,,53999848,44698032,48251471,52911263,0,ERX604038,ERS557922,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.75262,,0.42794,,0.83619,,0.5624,,29,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15544,ERR647601,ERX604037,ERS557921,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Female 008,SAMEA2796306,UNIVERSITY OF AMSTERDAM,Alias:Female 008|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:25Z|INSDC status:public|SRA accession:ERS557921|Sample Name:ERS557921|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 6,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_008.fastq.gz,fastq,190251948.0,6082600.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 6,0:31.28,A:50176174;C:43027879;G:47458847;T:49589048;N:0,31,,,,50176174,43027879,47458847,49589048,0,ERX604037,ERS557921,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.72654,,0.373,,0.82785,,0.52436,,25,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15545,ERR647600,ERX604036,ERS557920,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Female 007,SAMEA2796305,UNIVERSITY OF AMSTERDAM,Alias:Female 007|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:24Z|INSDC status:public|SRA accession:ERS557920|Sample Name:ERS557920|Title:Male vs Female|dev stage:Adult|sex:female|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 5,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_007.fastq.gz,fastq,214503694.0,6990446.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 5,0:30.69,A:59354819;C:47472262;G:51306173;T:56370440;N:0,30,,,,59354819,47472262,51306173,56370440,0,ERX604036,ERS557920,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74272,,0.45587,,0.83161,,0.53444,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15546,ERR647599,ERX604035,ERS557919,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 014,SAMEA2796304,UNIVERSITY OF AMSTERDAM,Alias:Male 014|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:24Z|INSDC status:public|SRA accession:ERS557919|Sample Name:ERS557919|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 4,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_005.fastq.gz,fastq,235098531.0,7522781.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 4,0:31.25,A:58178492;C:54009752;G:64159987;T:58750300;N:0,31,,,,58178492,54009752,64159987,58750300,0,ERX604035,ERS557919,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.73752,,0.19698,,0.86665,,0.58697,,13,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15547,ERR647598,ERX604034,ERS557918,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 011,SAMEA2796303,UNIVERSITY OF AMSTERDAM,Alias:Male 011|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:24Z|INSDC status:public|SRA accession:ERS557918|Sample Name:ERS557918|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 3,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_004.fastq.gz,fastq,223142261.0,6553993.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 3,0:34.05,A:55488952;C:50941034;G:58123716;T:58588559;N:0,34,,,,55488952,50941034,58123716,58588559,0,ERX604034,ERS557918,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.74686,,0.2139,,0.86996,,0.55375,,11,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15548,ERR647597,ERX604033,ERS557917,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 006,SAMEA2796302,UNIVERSITY OF AMSTERDAM,Alias:Male 006|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:24Z|INSDC status:public|SRA accession:ERS557917|Sample Name:ERS557917|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 2,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_002.fastq.gz,fastq,166401146.0,5656405.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 2,0:29.42,A:41137490;C:38824883;G:44865980;T:41572793;N:0,29,,,,41137490,38824883,44865980,41572793,0,ERX604033,ERS557917,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.69452,,0.18245,,0.87044,,0.58162,,11,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15549,ERR647596,ERX604032,ERS557916,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 003,SAMEA2796301,UNIVERSITY OF AMSTERDAM,Alias:Male 003|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:38:23Z|INSDC status:public|SRA accession:ERS557916|Sample Name:ERS557916|Title:Male vs Female|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 1,RID0035,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0035_001.fastq.gz,fastq,167146177.0,6380638.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:37:59:568 1,0:26.20,A:43620211;C:36811253;G:43301042;T:43413671;N:0,26,,,,43620211,36811253,43301042,43413671,0,ERX604032,ERS557916,ERA363846,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.70048,,0.18034,,0.88075,,0.55658,,11,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15551,ERR647594,ERX604030,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 6,RID0011,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0011_015.fastq.gz,fastq,273349184.0,9019669.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 6,0:30.31,A:74069549;C:59041449;G:64551451;T:75686735;N:0,30,,,,74069549,59041449,64551451,75686735,0,ERX604030,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78759,,0.26081,,0.90989,,0.51416,,29,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15552,ERR647589,ERX604025,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 1,RID0011,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0011_010.fastq.gz,fastq,54651692.0,2000589.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 1,0:27.32,A:16624629;C:13894132;G:10557585;T:13575346;N:0,27,,,,16624629,13894132,10557585,13575346,0,ERX604025,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.11072,,0.02655,,0.97749,,0.53916,,26,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15553,ERR647590,ERX604026,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 2,RID0011,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0011_011.fastq.gz,fastq,47051190.0,1414933.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 2,0:33.25,A:12984359;C:11329853;G:10330928;T:12406050;N:0,33,,,,12984359,11329853,10330928,12406050,0,ERX604026,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.36871,,0.10094,,0.9483,,0.51008,,40,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15554,ERR647592,ERX604028,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 4,RID0011,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0011_013.fastq.gz,fastq,394812059.0,13329274.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 4,0:29.62,A:108705027;C:84131955;G:92090437;T:109884640;N:0,29,,,,108705027,84131955,92090437,109884640,0,ERX604028,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.65205,,0.21183,,0.91977,,0.52643,,21,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15555,ERR647593,ERX604029,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 5,RID0011,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0011_014.fastq.gz,fastq,143238806.0,4225461.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 5,0:33.90,A:38374880;C:31424768;G:33687670;T:39751488;N:0,33,,,,38374880,31424768,33687670,39751488,0,ERX604029,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.78469,,0.26587,,0.92178,,0.51694,,80,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
15556,ERR647591,ERX604027,ERS557914,ERP007147,PRJEB7420,Two Sets of Synthetic Spike in Controls for Size Selection and Data Normalisation in small RNA seq,ena-STUDY-UNIVERSITY OF AMSTERDAM-01-10-2014-14:02:22:856-622,Other,There is an increasing interest in complementing standard RNA seq experiments with small RNA expression data to obtain a comprehensive view of the transcriptome. Two aspects need to be considered when small RNA seq sRNA seq is used. First  sRNA seq protocols are size selective and typically optimized for sequencing miRNAs. Second  given the dynamic composition of the small RNA fraction a reliable normalization strategy is needed to identify differentially expressed sRNAs. To address both issues we here present two sets of synthetic RNA spike in controls for monitoring size selectivity and for performing normalization. Size spike ins comprising 18 oligoribonucleotides 10–300 nucleotides were designed and tested using controlled modifications to the size selectivity of sRNA seq. As an applied example  the loss of RNA molecules <30 nucleotides during small RNA isolation from zebrafish oocytes is demonstrated. Normalization spike ins comprising 19 oligoribonucleotides were designed to use as an external reference for DESeq normalization. Spike in based normalization improved the quantification of predetermined fold changes. Lastly  sRNA seq on female and male zebrafish demonstrated that the higher miRNA content in males was correctly preserved post spike in based normalization.,,,,Male 001,SAMEA2796299,UNIVERSITY OF AMSTERDAM,Alias:Male 001|ENA checklist:ERC000011|INSDC center alias:UNIVERSITY OF AMSTERDAM|INSDC center name:UNIVERSITY OF AMSTERDAM|INSDC first public:2014 11 29T17:02:28Z|INSDC last update:2014 10 01T14:42:44Z|INSDC status:public|SRA accession:ERS557914|Sample Name:ERS557914|Title:Male ZF|dev stage:Adult|sex:male|strain:ABxTL,,,,,,,,,Ion Torrent Proton sequencing,ena EXPERIMENT UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 3,RID0011,1,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,ERP007147,Ion Torrent Proton sequencing,ENA FIRST PUBLIC:2014 11 29|ENA LAST UPDATE:2018 11 16,RID0011_012.fastq.gz,fastq,55541174.0,1649692.0,ena RUN UNIVERSITY OF AMSTERDAM 01 10 2014 14:02:18:976 3,0:33.67,A:16076639;C:14164415;G:11139997;T:14160123;N:0,33,,,,16076639,14164415,11139997,14160123,0,ERX604027,ERS557914,ERA363842,UNIVERSITY OF AMSTERDAM,UNIVERSITY OF AMSTERDAM,1,0.16692,,0.04528,,0.96384,,0.52823,,17,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2014-10-01,Adult,Adult,Undetermined,Undetermined
41418,SRR4423118,SRX2245302,SRS1745860,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult FT Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:female|tissue:tail|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult female tail,172 5,172 5,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,femaletailRID0172BC05smallZF.fastq,fastq,491055734.0,7690105.0,femaletailRID0172BC05smallZF.fastq,0:63.86,A:114732043;C:132287469;G:130972143;T:113064079;N:0,63,,,,114732043,132287469,130972143,113064079,0,SRX2245302,SRS1745860,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.82246,,0.13521,,0.91303,,0.63226,,43,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Tail,Multi-system
41419,SRR4423117,SRX2245301,SRS1745860,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult FT Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:female|tissue:tail|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: Adult female tail,172 3,172 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,femaletailRID0172BC03largeZF.fastq,fastq,1414932187.0,9757587.0,femaletailRID0172BC03largeZF.fastq,0:145.01,A:343007105;C:362895564;G:422320111;T:286709407;N:0,145,,,,343007105,362895564,422320111,286709407,0,SRX2245301,SRS1745860,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.96057,,0.21796,,0.95177,,0.76663,,141,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Tail,Multi-system
41421,SRR4423115,SRX2245299,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,94 3,94 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0094BC03smallZF.fastq,fastq,697814234.0,14408051.0,maleRID0094BC03smallZF.fastq,0:48.43,A:165337411;C:177790468;G:184204311;T:170482044;N:0,48,,,,165337411,177790468,184204311,170482044,0,SRX2245299,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.70426,,0.16215,,0.91027,,0.5459,,120,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
41423,SRR4423113,SRX2245297,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,RNA Seq of Zebrafish: Adult male whole body,99 5,99 5,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific.,,,RNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0099BC05LargeZF.fastq,fastq,3606425618.0,40350582.0,maleRID0099BC05LargeZF.fastq,0:89.38,A:900873268;C:899774590;G:1079098037;T:726679723;N:0,89,,,,900873268,899774590,1079098037,726679723,0,SRX2245297,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.90069,,0.21287,,0.95726,,0.72186,,53,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,cdna_unspecified,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
41425,SRR4423111,SRX2245295,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,88 3,88 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0088BC03smallZF.fastq,fastq,523776538.0,11118832.0,maleRID0088BC03smallZF.fastq,0:47.11,A:123827431;C:133478804;G:138882662;T:127587641;N:0,47,,,,123827431,133478804,138882662,127587641,0,SRX2245295,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.69556,,0.16368,,0.9093,,0.54838,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
41427,SRR4423109,SRX2245293,SRS1745859,SRP091534,PRJNA347637,Danio rerio and Xenopus laevis Raw sequence reads,PRJNA347637,Other,To study the transcriptome during development,,,,,Adult MWB Dr,,strain:not applicable|isolate:not applicable|breed:ABTL|cultivar:not applicable|ecotype:not applicable|age:not applicable|dev stage:Adult|sex:male|tissue:whole body|BioSampleModel:Model organism or animal,,,,,,,,,miRNA Seq of Zebrafish: Adult male whole body,93 3,93 3,Libraries were generated according to the manufacturers’ protocols using the Ion Total RNA Seq Kit v2 and the Ion Xpress™ RNA Seq bar coding kit Thermo Fisher Scientific. A few modifications were made during purification steps in the small RNAseq to allow sequencing of longer RNAs up to 200 nt than with standard sRNA protocols. Namely: 153 µl ethanol instead of 120 µl during purification of cDNA and 134 µl ethanol instead of 110 µl in protocol.,,,miRNA-Seq,TRANSCRIPTOMIC,cDNA,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP091534,,,maleRID0093BC03smallZF.fastq,fastq,692750598.0,14286031.0,maleRID0093BC03smallZF.fastq,0:48.49,A:164412063;C:176380331;G:182539801;T:169418403;N:0,48,,,,164412063,176380331,182539801,169418403,0,SRX2245293,SRS1745859,SRA485147,Universiteit van Amsterdam|SILS,Universiteit van Amsterdam,1,0.70738,,0.16645,,0.90948,,0.55306,,22,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,small_rna,unknown,bulk,unknown,unknown,,Netherlands,2016-10-19,Adult,Adult,Trunk,Surface Structure
59501,SRR11924323,SRX8469995,SRS6770646,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,Adult tail 2,GSM4591062,,source name:adult tail trunk|tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA,Adult tail 2,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,adult tail trunk,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591062,GSM4591062: Adult tail 2; Danio rerio; OTHER,GSM4591062,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591062,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,Adult_tail_2.bam GSE151797_Reference_sequence.fa,bam bam,156647953.0,5517527.0,GSM4591062 r1,0:28.39,A:32903673;C:49609293;G:39096775;T:35038212;N:0,28,,,,32903673,49609293,39096775,35038212,0,SRX8469995,SRS6770646,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.80662,,0.20653,,0.88722,,0.58074,,37,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Adult,Adult,Multi-tissue,Multi-system
59502,SRR11924321,SRX8469994,SRS6770645,SRP265951,PRJNA637293,The shift from early to late types of ribosomes in zebrafish development involves changes at a subset of rRNA 2' O Me sites,GSE151797,Other,A sequencing based profiling method RiboMeth seq for ribose methylations was used to study methylation patterns during Zebrafish Danio rerio development Overall design: All samples were analyzed in biological triplicates  except for adult tail trunk that was in duplicate.,,pubmed:32912962,,Adult tail 1,GSM4591061,,source name:adult tail trunk|tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA,Adult tail 1,Library strategy: RiboMeth seq Barcode separation using python script Adaptor trimming using Cutadapt v. 2.0 Mapping to rRNA reference sequence using Bowtie2 v. 2.3.4.1 Counting read ends and calculating RiboMeth seq scores using python scripts The output FASTA files from small RNA seq were merged and used as the basis of the SNORD search and rRNA interaction prediction. Initially  SNORDs were identified by running the merged FASTA file through snoScan Schattner et al. 2005 against zebrafish early  and late rRNA reference sequences Locati et al. 2017. Genome build: early and late zebrafish rRNA locati et al. The reference sequences are available in the FASTA file on the series record. Supplementary files format and content: MS Excel file contains five prime and three prime read count and calculated RiboMeth seq score at all positions in the rRNA sequence.,adult tail trunk,,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,,tissue:adult tail trunk|rna fraction:size fractionated 20 40 nt whole cell RNA,GSM4591061,GSM4591061: Adult tail 1; Danio rerio; OTHER,GSM4591061,,1,Tissues were homogenized and whole cell RNA was extracted using Qiazol Qiagen according to the manufacturer. RiboMeth seq: 5 10 ug of RNA was partially degraded by alkaline at denaturing temperatures. The size fraction 20 40 nt was purified on gels and linkers added using a system relying on a modified Arabidopsis tRNA ligase joining 2' three prime cyclic phosphate and five prime phosphate ends. The library fragments were then sequenced on the Ion Proton platform. See Birkedal U  Christensen Dalsgaard M  Krogh N  Sabarinathan R  Gorodkin J  Nielsen H. Profiling of ribose methylations in RNA by high throughput sequencing. Angewandte Chemie. 2015;542:451 5 for detailed description,GEO Accession:GSM4591061,OTHER,TRANSCRIPTOMIC,other,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP265951,,intentional duplicate,Adult_tail_1.bam GSE151797_Reference_sequence.fa,bam bam,50029636.0,1968329.0,GSM4591061 r1,0:25.42,A:9571393;C:14825016;G:13276309;T:12356918;N:0,25,,,,9571393,14825016,13276309,12356918,0,SRX8469994,SRS6770645,SRA1083099,GEO,"RNA Group - Prof. Henrik Nielsen, Department of Cellular and Molecular Medicine, University of Copenhagen",1,0.46312,,0.12127,,0.91806,,0.67424,,44,,B,,usable mapping rate,ion_torrent,ion_torrent,5prime,small_rna,unknown,bulk,unknown,unknown,,Denmark,2020-06-04,Adult,Adult,Multi-tissue,Multi-system
62854,SRR13440556,SRX9853978,SRS8035408,SRP301838,PRJNA691414,Transcriptomic analysis of GD treated zebrafish liver,PRJNA691414,Other,Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.,,,,Zebrafish liver from AB strain,GD DIO Zebrafish,,strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: adult female liver,DIO GD 4,DIO GD 4,DIO with GD treatment,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP301838,,,DIO_GD-4,fastq,4457846127.0,35434325.0,DIO GD 4,0:125.81,A:1132283216;C:1070720177;G:1157322546;T:1097520188;N:0,125,,,,1132283216,1070720177,1157322546,1097520188,0,SRX9853978,SRS8035408,SRA1184195,Mie University|Graduate School of Regional Innovation Studies,Mie University,1,0.61358,,0.13617,,0.87896,,0.27516,,178,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2021-01-14,Adult,Adult,Liver,Liver and Biliary System
62855,SRR13440557,SRX9853977,SRS8035408,SRP301838,PRJNA691414,Transcriptomic analysis of GD treated zebrafish liver,PRJNA691414,Other,Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.,,,,Zebrafish liver from AB strain,GD DIO Zebrafish,,strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: adult female liver,DIO GD 3,DIO GD 3,DIO with GD treatment,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP301838,,,DIO_GD-3,fastq,2209140756.0,21626130.0,DIO GD 3,0:102.15,A:583812333;C:487262915;G:584943625;T:553121883;N:0,102,,,,583812333,487262915,584943625,553121883,0,SRX9853977,SRS8035408,SRA1184195,Mie University|Graduate School of Regional Innovation Studies,Mie University,1,0.63225,,0.1658,,0.86379,,0.37214,,92,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2021-01-14,Adult,Adult,Liver,Liver and Biliary System
62856,SRR13440558,SRX9853976,SRS8035408,SRP301838,PRJNA691414,Transcriptomic analysis of GD treated zebrafish liver,PRJNA691414,Other,Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.,,,,Zebrafish liver from AB strain,GD DIO Zebrafish,,strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: adult female liver,DIO GD 2,DIO GD 2,DIO with GD treatment,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP301838,,,DIO_GD-2,fastq,1777323103.0,18933651.0,DIO GD 2,0:93.87,A:464601836;C:413760770;G:460577599;T:438382898;N:0,93,,,,464601836,413760770,460577599,438382898,0,SRX9853976,SRS8035408,SRA1184195,Mie University|Graduate School of Regional Innovation Studies,Mie University,1,0.65849,,0.15297,,0.84135,,0.3349,,101,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2021-01-14,Adult,Adult,Liver,Liver and Biliary System
62857,SRR13440559,SRX9853975,SRS8035408,SRP301838,PRJNA691414,Transcriptomic analysis of GD treated zebrafish liver,PRJNA691414,Other,Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.,,,,Zebrafish liver from AB strain,GD DIO Zebrafish,,strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: adult female liver,DIO GD 1,DIO GD 1,DIO with GD treatment,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP301838,,,DIO_GD-1,fastq,3107066238.0,25095995.0,DIO GD 1,0:123.81,A:793240480;C:738189877;G:777063754;T:798572127;N:0,123,,,,793240480,738189877,777063754,798572127,0,SRX9853975,SRS8035408,SRA1184195,Mie University|Graduate School of Regional Innovation Studies,Mie University,1,0.7426,,0.17704,,0.89051,,0.25099,,52,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2021-01-14,Adult,Adult,Liver,Liver and Biliary System
62858,SRR13440560,SRX9853974,SRS8035408,SRP301838,PRJNA691414,Transcriptomic analysis of GD treated zebrafish liver,PRJNA691414,Other,Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.,,,,Zebrafish liver from AB strain,GD DIO Zebrafish,,strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: adult female liver,DIO 4,DIO 4,Diet incuced obesity DIO,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP301838,,,DIO-4,fastq,2329004075.0,20271175.0,DIO 4,0:114.89,A:567452533;C:570566957;G:621549245;T:569435340;N:0,114,,,,567452533,570566957,621549245,569435340,0,SRX9853974,SRS8035408,SRA1184195,Mie University|Graduate School of Regional Innovation Studies,Mie University,1,0.84548,,0.27189,,0.86198,,0.45426,,122,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2021-01-14,Adult,Adult,Liver,Liver and Biliary System
62859,SRR13440561,SRX9853973,SRS8035408,SRP301838,PRJNA691414,Transcriptomic analysis of GD treated zebrafish liver,PRJNA691414,Other,Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.,,,,Zebrafish liver from AB strain,GD DIO Zebrafish,,strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: adult female liver,DIO 3,DIO 3,Diet incuced obesity DIO,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP301838,,,DIO-3,fastq,2346162628.0,19400931.0,DIO 3,0:120.93,A:579812559;C:570332195;G:613738317;T:582279557;N:0,120,,,,579812559,570332195,613738317,582279557,0,SRX9853973,SRS8035408,SRA1184195,Mie University|Graduate School of Regional Innovation Studies,Mie University,1,0.78629,,0.25304,,0.89041,,0.35231,,150,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2021-01-14,Adult,Adult,Liver,Liver and Biliary System
62860,SRR13440562,SRX9853972,SRS8035408,SRP301838,PRJNA691414,Transcriptomic analysis of GD treated zebrafish liver,PRJNA691414,Other,Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.,,,,Zebrafish liver from AB strain,GD DIO Zebrafish,,strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: adult female liver,DIO 2,DIO 2,Diet incuced obesity DIO,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP301838,,,DIO-2,fastq,3553599859.0,32601495.0,DIO 2,0:109.00,A:888818483;C:851068166;G:947933039;T:865780171;N:0,109,,,,888818483,851068166,947933039,865780171,0,SRX9853972,SRS8035408,SRA1184195,Mie University|Graduate School of Regional Innovation Studies,Mie University,1,0.86167,,0.31911,,0.86206,,0.66264,,174,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2021-01-20,Adult,Adult,Liver,Liver and Biliary System
62861,SRR13440563,SRX9853971,SRS8035408,SRP301838,PRJNA691414,Transcriptomic analysis of GD treated zebrafish liver,PRJNA691414,Other,Globin digest is a bioactive oligopeptide derived from porcine hemoglobin proteins. We orally administrated GD to diet induced zebrafish fish and performed RNA seq using the liver of zebrafish with or without xxx treatment.,,,,Zebrafish liver from AB strain,GD DIO Zebrafish,,strain:AB|age:3 month|sex:female|tissue:liver|disease:Obesity|BioSampleModel:Model organism or animal,,,,,,,,,RNA seq of Danio rerio: adult female liver,DIO 1,DIO 1,Diet incuced obesity DIO,,,RNA-Seq,TRANSCRIPTOMIC,PCR,SINGLE,ION_TORRENT,Ion Torrent Proton,,SRP301838,,,DIO-1,fastq,2554201974.0,21594302.0,DIO 1,0:118.28,A:631716258;C:620459753;G:664379409;T:637646554;N:0,118,,,,631716258,620459753,664379409,637646554,0,SRX9853971,SRS8035408,SRA1184195,Mie University|Graduate School of Regional Innovation Studies,Mie University,1,0.77174,,0.21322,,0.89962,,0.33158,,240,,B,,usable mapping rate,ion_torrent,ion_torrent,unknown,random_priming,unknown,bulk,unknown,unknown,,Japan,2021-01-20,Adult,Adult,Liver,Liver and Biliary System